Did COVID-19 precautions harm our immune systems?

The newsletter where we discuss the differences between Microbes and Pathogens, the benefits of the microbiome, stages of infectious disease and what this all means in regards to today's world.

It’s been a good chunk of time since my last newsletter. Mostly because the spring semester started and my children are on a rotation of winter illness. I’ve been spending most of this winter coated in snot. Today though, the kids are finally healthy again after getting a non COVID, non Flu and non RSV virus. So I wanted to tackle a common misconception - that getting sick is “good” for you.

I’ve covered this a bit before in this Instagram post, but thought it was worth exploring a bit more here. So let’s dive in!

Microbes vs. Pathogens

One of the very first things we cover in the microbiology class I teach is the difference between microbes and pathogens. People tend to equate them, which is not true.

Microbes are organisms that require a microscope to be seen.

Typically these are things like bacteria, viruses, protozoa, fungus, worms and others. Many of these are harmless to humans. They may impact other animals or plants. Some actually are beneficial to us and live in and on - these help form something we call our microbiome.

However, thanks to things like COVID-19, influenza, Strep throat and MRSA we all know that not all microbes are harmless. This is where the term pathogen comes in.

A pathogen is a microbe that causes disease. So all pathogens are microbes, but not all microbes are pathogens!

What is further confusing is the use of “germ”. When people use this term some mean any microbe -pathogenic or not. Others are referring to pathogens. So it can quickly get confusing to parse out what is actually being discussed, because their is an important difference!

In my house, my toddler calls good microbes “happy germs” and pathogens “angry germs”.

Exposure to Microbes Matter

Microbes are everywhere in our environment - on the surfaces we touch, in the air, in the dirt we play in. Most of these are non-pathogenic, so they won’t make you sick. However, we are increasingly learning that exposure to microbes are important. Especially in the early years of life as children are developing their microbiome.

Your microbiome - the collection of microbes that live in and on you - influence so many things you probably aren’t aware of. They help stimulate our immune system, they help us digest our food and synthesize vitamins. They also have been found to have a role in our mental health.

The importance of the microbiome is one reason why the hygiene hypothesis is often misunderstood and misinterpreted. Originally, this hypothesis was often used to say that exposure to germs (e.g. pathogens in this case) was necessary to develop an immune system, but this was coined before we truly understood the importance of our microbiome.

We now know its importance, and we now know about the harm pathogens can cause - both in the short term, but also due to long term complications known as sequalae. For example, having gotten the virus (EBV) that causes mononucleosis, makes you more at risk for Burkitt's lymphoma and multiple sclerosis. Having had COVID-19 puts you at risk for long COVID, and other health complications.

What is now thought to be necessary is exposure to good microbes (or happy germs as my toddler says). New data is suggesting that consistent exposure to these good microbes, especially early in life, can help reduce the risk of allergies and similar health issues. For example, children who grow up on farms - where microbes are plenty - are somewhat protected from allergies.

Exposure to good microbes early in life can be aided through a varied diet, playing in the dirt, getting outside etc… These exposures can all help form a diverse microbiome.

Another important factor is to reduce the improper use of antibiotics. Antibiotics are lifesaving, but should only be used when needed for bacterial infections. This is critical for many reasons, including helping to reduce the development of antibiotic resistance and the risk of killing the good microbes in our microbiome.

One remaining question though is what constitutes a “good” microbiome? We are starting to find that variations in the microbiome can be associated with disease, but we are sill very unsure what makes up a good one. In reality, it likely varies significantly, so more research is needed.

How does your immune system respond to pathogens?

There is now a concerning and pervasive misunderstanding circulating in this pandemic era. It is the claim that our mitigation methods have harmed our immune systems. Proponents of this argument are suggesting that you need to get sick to have a healthy immune system - which is false.

So now I’m going to discuss what happens when you are exposed to a pathogen.

Image modified from Biorender template by me!

1. Incubation period: This is the time where you’ve been exposed, and the pathogen is getting ready to start increasing in number. At this time your immune system is not aware, and you have no symptoms.

2. Prodromal period: This is the time where the pathogen has started replicating, and your immune system may just be realizing what is going on. Mild symptoms can start here.

3. Illness. This is the phase where you are sick. You likely are experiencing many symptoms. Both due to your immune system now responding and due to the fact that the pathogen now is prevalent in higher numbers.

4. Decline. This is the phase where your immune response has won! It is killing off the pathogen.

5. Convalescence. This is the recovery period post infection. Where your body is trying to repair any damage caused by the infection and you may still have lingering symptoms (like a cough). Your adaptive immune system is going to now form memory cells to protect you if you’re exposed with the same pathogen again. For some, long term consequences can result that persist long after initial infection.

So, when you are first encountering a pathogen (or vaccination for that pathogen) your immune system is “naïve” which means it hasn’t encountered the pathogen before. Once you’ve been infected with a pathogen you become ill, then your immune system learns to recognize that pathogen. This memory can then can protect you if you reencounter the same pathogen again. Though how long immune system memory lasts varies from pathogen to pathogen.

Getting sick with one pathogen does not protect you from other unrelated pathogens or make your immune system better, it just means you may be protected against that specific pathogen if you encounter it again.

So, have COVID-19 precautions hurt our immune system?

During the early days of the COVID-19 pandemic when mitigation methods were in place, we did see decreases in infectious diseases circulating. For example, we saw less flu and less RSV. Some people are arguing this was bad, because it harmed our immune system. As discussed above, pathogens are not good for our immune system. However, exposure to pathogens (or vaccination for pathogens) is required to develop immunity to those specific pathogens. Thus, its important to realize, that its not that these precautions harmed our immune system, simply that people had naïve immune systems so got sick once exposed to these pathogens.

This is why children who first enter daycare or school often get sick a lot in the first few years. They haven’t encountered pathogens before, so they are naïve to those pathogens.

Now, one interesting thing to note is that it may have actually been beneficial that children delayed their first exposure to pathogens. Especially those under 12 months of age. We have data that shows that infants under 12 months who get RSV are more at risk of developing asthma afterwards. Thus, delaying infection may actually reduce rates of asthma in those children. We need to remember that pathogen exposure develops immunity to that pathogen, BUT can also have significant long term impacts. Unfortunately, pathogen exposure is somewhat unavoidable, but that does not mean we should WANT our kids to get sick.

What is true though, is that a diverse microbiome is good for your immune system, but that can be achieved through a variety of lifestyle decisions and is separate from exposure to pathogens and getting sick.

So what is not clear, is how microbiomes may have changed during the pandemic. I know my children still have played outside in dirt, have eaten off the floor at home, have played with dogs and have gotten sick from daycare. Many people moved outdoors more during the pandemic, which may have benefitted microbiomes. People were sick less, which means they may have used less antibiotics than they would have otherwise - thus preserving their microbiome. We also do not know what actually constitutes a “good” microbiome, and one can argue many people may have had bad microbiomes pre-pandemic.

Katherine Wu has a good article on this that highlights how microbiomes have likely changed, but we don’t know how yet or the impact of that.

Given the fact that COVID-19 can cause significant long term effects, delaying infection through precautions was not a bad decision. We still do not truly know the long term risks of COVID-19, or how vaccination or repeat infections may change that.

So, my family and I will continue to do what we can to avoid repeat COVID infections. We will play outside and with animals. We will eat lots of fruits, fermented foods and vegetables. I won’t panic if the kids eat off the floor. But I also will not want them to get sick. I won’t seek out pathogen exposure. Some sickness is inevitable, especially when pathogens encounter a naïve immune system. But it is not required to be healthy. Don’t let anyone tell you otherwise!

If you have questions feel free to reach out in comments, via email or on Instagram!